(this section is incomplete)
The boss: Ganondorf
Navi is held back by Ganon's evilness so you cannot use Z-targeting during this battle. Simply stand on any of the outer blocks and let Ganon shoot at you. Send the magic back to him and he'll brush it off with his cloak, but after a few such blows he'll be overwhelmed with the energy and will pause in his attacks. At this point hit him with a light arrow, then jump onto the platform and slash him to pieces. Jump back to the squares and repeat.
If you need health or magic drop down to the bottom area where the pots are.
Eventually you'll kill Ganon. Unfortunately with his dying breath he tries to bring the castle down around him, intending to bury you alive!
Escaping the Castle
Follow Zelda down through the different levels of the castle. Be sure to stand right in front of each grille in order to trigger her to open it. Most of the time you can second-guess her and run on ahead. However if you get hit by falling debris Zelda will gasp and remain where she is, so you'll need to go back for her.
At one point Zelda will be encircled with flames and two Stalfos appear. Destroy them quickly or a third will appear! The flames will then vanish and Zelda will moult hearts. Go up to her and get them if you need them, then continue on your way.
Eventually you'll come down the stairs and reach a doorway with bright white light outside. Go through and you're back outside. You'll now see the castle slowly crumble down into a pile of rubble.
Zelda now goes on about how everything will get back to normal when suddenly there comes a noise from the rubble. She sends you to investigate.
Walk over and Ganondorf will emerge from the rubble and somehow transform into his super-form, Ganon. Ganon knocks the Master Sword out of Link's hands, leaving him without his most effective boss-killing weapon.
The boss: Ganon
This time you've got your trusty Z-targeting back. Strike Ganon between the eyes with the light arrows leaving him stunned. This makes his vulnerable tail drop down within reach. Quickly target it and rush in behind him to slash it to pieces. If you don't have the Biggoron Sword the Megaton Hammer will also work. If you need a magic refill just head to one of the crumbled walls and let Ganon strike at it, revealing the bottles.
Once he's down rush over and get the Master Sword, and equip it, then go and hit him quickly before he gets up (the more blows the better). Then repeat the same process until he's down yet again.
This time however Zelda will hold him still with her powers and tell you to deliver the final blow. Simply walk up to him and slash, and it's all over.